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how to find new transcript from bam file?

Hi, I have many BAM and BED files. I am looking some novel transcripts (missed) from my BAM file. Is there any way to extract new transcripts from my BAM file. any suggestion

next-gen alignment rna-seq
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updated by Federico Giorgi Federico Giorgi • written by PK • PK

1 answer

Cufflinks used to be the most popular, but I would suggest StringTie (also from Johns Hopkins University), because it is more accurate for intronic and intron-retaining transcripts. They both require a BAM file as input and an optional transcript track annotation file (GFF3 or GTF)

Cufflinks

StringTie

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written by Federico Giorgi Federico Giorgi

Thanks for your suggestion. The problem is i try to find smallRNA and I already tried with cufflinks but not satisfied. I can try stringtie.

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written by PK • PK

Do you try to get smallRNAs from standard RNA-seq or from smallRNA-seq?

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written by ATpoint ATpoint

it's very hard to say because we prepared the samples in a different way. it reduces the rRNAs from 80% to 20% and my snoRNAs are enriched from 5% to 30%.

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written by PK • PK

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